RIP-seq library prep - single or paired-end reads?

lre1234

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RIP-seq library prep - single or paired-end reads?

10-13-2016, 06:05 AM

Hi all,
I'm going to be helping a colleague with analyzing some RIP-seq data. We just had a question regarding the library prep protocol. Specifically, is it better to use paired-end or single-ended sequencing. My thought is to just use single-end 75bp reads. Does anyone have experience and/or thoughts about this as to which would be a better choice?
Thanks
Tags: library perparation, paired end read, rip-seq, single end reads
BrianJames

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10-13-2016, 11:19 AM

No experience with RIP-seq (yet), but it is a pretty fragmented starting material. I'm not sure you would get any more/better data from paired end sequencing.

Brian
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